Class

dagr.tasks.gatk

IndelRealignment

Related Doc: package gatk

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class IndelRealignment extends Pipeline

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. IndelRealignment
  2. Pipeline
  3. LazyLogging
  4. Task
  5. Dependable
  6. AnyRef
  7. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new IndelRealignment(in: Seq[PathToBam], out: DirPath, ref: PathToFasta, known: Seq[PathToVcf] = Nil, intervals: Option[PathToIntervals] = None)

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    CLP constructor for testing and manual use, since there's no easy way to provide a map on the CLI.

  2. new IndelRealignment(bams: Map[PathToBam, PathToBam], ref: PathToFasta, known: Seq[PathToVcf], intervals: Option[PathToIntervals])

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  3. def !=>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  4. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  5. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to any2stringadd[IndelRealignment] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  6. def ->[B](y: B): (IndelRealignment, B)

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to ArrowAssoc[IndelRealignment] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  7. def ::(other: Task): MultiTask

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    Definition Classes
    Task

  8. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  9. def ==>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  10. def ==>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  11. def addTask(task: Task): task.type

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    Definition Classes
    Pipeline

  12. def addTasks(task: Task*): Unit

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    Definition Classes
    Pipeline

  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  14. val bams: Map[PathToBam, PathToBam]

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  15. def build(): Unit

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    Constructs a mini pipeline that runs RealignerTargetCreator and IndelRealigner on multiple samples together.

    Constructs a mini pipeline that runs RealignerTargetCreator and IndelRealigner on multiple samples together.

    Definition Classes
    IndelRealignment → Pipeline

  16. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  17. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  18. def ensuring(cond: (IndelRealignment) ⇒ Boolean, msg: ⇒ Any): IndelRealignment

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to Ensuring[IndelRealignment] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  19. def ensuring(cond: (IndelRealignment) ⇒ Boolean): IndelRealignment

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to Ensuring[IndelRealignment] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  20. def ensuring(cond: Boolean, msg: ⇒ Any): IndelRealignment

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to Ensuring[IndelRealignment] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  21. def ensuring(cond: Boolean): IndelRealignment

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to Ensuring[IndelRealignment] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  22. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  23. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  24. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  25. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to StringFormat[IndelRealignment] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  26. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  27. final def getTasks: Traversable[_ <: Task]

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    Definition Classes
    Pipeline → Task

  28. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  29. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  30. val known: Seq[PathToVcf]

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  31. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  32. var name: String

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    Definition Classes
    Task

  33. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  34. final def notify(): Unit

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    Definition Classes
    AnyRef

  35. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  36. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  37. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  38. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  39. def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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    Definition Classes
    Task

  40. val root: Dependable

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    Definition Classes
    Pipeline

  41. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  42. def toString(): String

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    Definition Classes
    AnyRef → Any

  43. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  44. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  45. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  46. def withName(name: String): IndelRealignment.this.type

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    Definition Classes
    Task

  47. def →[B](y: B): (IndelRealignment, B)

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    Implicit information
    This member is added by an implicit conversion from IndelRealignment to ArrowAssoc[IndelRealignment] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Pipeline

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from IndelRealignment to any2stringadd[IndelRealignment]

Inherited by implicit conversion StringFormat from IndelRealignment to StringFormat[IndelRealignment]

Inherited by implicit conversion Ensuring from IndelRealignment to Ensuring[IndelRealignment]

Inherited by implicit conversion ArrowAssoc from IndelRealignment to ArrowAssoc[IndelRealignment]

Ungrouped